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- PDB-1qc5: I Domain from Integrin Alpha1-Beta1 -

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Basic information

Entry
Database: PDB / ID: 1qc5
TitleI Domain from Integrin Alpha1-Beta1
Components(PROTEIN (ALPHA1 BETA1 INTEGRIN)) x 2
KeywordsCELL ADHESION / INTEGRIN
Function / homology
Function and homology information


cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Other semaphorin interactions / CHL1 interactions / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / integrin complex / cell adhesion mediated by integrin ...cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Other semaphorin interactions / CHL1 interactions / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity / Smooth Muscle Contraction / Integrin cell surface interactions / collagen binding / neutrophil chemotaxis / cell-matrix adhesion / neuron projection morphogenesis / acrosomal vesicle / integrin-mediated signaling pathway / cell-cell adhesion / vasodilation / positive regulation of neuron apoptotic process / integrin binding / perikaryon / protein phosphatase binding / positive regulation of MAPK cascade / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site ...: / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDeivanayagam, C.C. / Narayana, S.V.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Trench-shaped binding sites promote multiple classes of interactions between collagen and the adherence receptors, alpha(1)beta(1) integrin and Staphylococcus aureus cna MSCRAMM.
Authors: Rich, R.L. / Deivanayagam, C.C. / Owens, R.T. / Carson, M. / Hook, A. / Moore, D. / Symersky, J. / Yang, V.W. / Narayana, S.V. / Hook, M.
History
DepositionMay 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ALPHA1 BETA1 INTEGRIN)
B: PROTEIN (ALPHA1 BETA1 INTEGRIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0634
Polymers43,0152
Non-polymers492
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.440, 96.350, 53.270
Angle α, β, γ (deg.)90.00, 104.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99992, -0.00578, -0.01165), (-0.0121, -0.08396, -0.996403), (-0.00479, 0.99645, -0.084027)
Vector: 15.765, -47.696, 52.091)

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Components

#1: Protein PROTEIN (ALPHA1 BETA1 INTEGRIN)


Mass: 21501.279 Da / Num. of mol.: 1 / Fragment: I-DOMAIN / Mutation: T137R, Q138S, P139S, T338G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P56199
#2: Protein PROTEIN (ALPHA1 BETA1 INTEGRIN)


Mass: 21513.334 Da / Num. of mol.: 1 / Fragment: I-DOMAIN / Mutation: T137R, Q138S, P139S, T338G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P56199
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MMEPEG2000, HEPES, SODIUM CHLORIDE, MAGNESIUM CHLORIDE, BETA-MERCAPTOETHANOL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K
Crystal
*PLUS
Density % sol: 35.3 %
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mMHEPES1drop
3200 mM1dropNaCl
45 mM1dropMgCl2
55 mMbeta-mercaptoethanol1drop
631 %PEG20001reservoir
750 mMHEPES1reservoir
8200 mM1reservoirNaCl
95 mM1reservoirMgCl2
105 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 140776 / Num. obs: 24698 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 24.1
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 8.1 / Rsym value: 0.209 / % possible all: 95.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 100 Å / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Num. measured all: 140776 / Biso Wilson estimate: 17.1 Å2
Reflection shell
*PLUS
Highest resolution: 1.99 Å / Lowest resolution: 2.07 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 8.1

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE A DOMAIN OF HUMAN COMPLEMENT FACTOR B

Resolution: 2→100 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1166602.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2434 9.9 %RANDOM
Rwork0.206 ---
all-24537 --
obs-24537 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.29 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å22.31 Å2
2---0.66 Å20 Å2
3---0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 2 229 3239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 388 9.6 %
Rwork0.232 3633 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 100 Å / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / Rfactor Rwork: 0.232

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